Ecological extinction is "the reduction of a species to such low abundance that, although it is still present in the community, it no longer interacts significantly with other species".

Ecological extinction stands out because it is the interaction ecology of a species that is important for conservation work. They state that "unless the species interacts significantly with other species in the community (e.g. it is an important predator, competitor, symbiont, mutualist, or prey) its loss may result in little to no adjustment to the abundance and population structure of other species".

This view stems from the neutral model of communities that assumes there is little to no interaction within species unless otherwise proven.

Estes, Duggins, and Rathburn (1989) recognize two other distinct types of extinction:

Robert Paine (1969) first came up with the concept of a keystone species while studying the effects of the predatory sea star Pisaster ochraceus, on the abundance of the herbivorous gastropod, Tegula funebralis. This study took place in the rocky intertidal habitat off the coast of Washington; Paine removed all Pisaster in 8m x 10m plots weekly while noting the response of Tegula for two years. He found that removing the top predator, in this case being Pisaster, reduced species number in the treatment plots. Paine defined the concept of a keystone species as a species that has a disproportionate effect on the community structure of an environment in relation to its total biomass. This keystone species effect forms the basis for the concept of ecological extinction.

The potential role of the sea otter as the keystone predator in near-shore kelp forests was evaluated by Estes et al. in a 1978 study. They compared the Rat and Near islands in the Aleutian islands to test if "sea otter predation controls epibenthic invertebrate populations (specifically sea urchins), and in turn releases the vegetation association from intense grazing". Estes and his colleagues found that different size structures and densities of sea urchins were correlated with the presence of sea otter populations, and because they are the principal prey of this keystone predator, the sea otters were most likely the main determinants of the differences in sea urchin populations. With high sea otter densities the herbivory of sea urchins in these kelp forest was severely limited, and this made competition between algal species the main determinant in survival. However, when sea otters were absent, herbivory of the sea urchins was greatly intensified to the point of decimation of the kelp forest community. This loss of heterogeneity serves as a loss of habitat for both fish and eagle populations that depend on the richly productive kelp forest environment. Historical over harvesting of sea otter furs has severely restricted their once wide-ranging habitat, and only today are scientists starting to see the implications of these local extinctions.

The California spiny lobster, or Panulirus interruptus, is a keystone predator that has a distinct role in maintaining species diversity in its habitat. Robles (1987) demonstrated experimentally that the exclusion of spiny lobsters from the intertidal zone habitats led to the competitive dominance of mussels (Mytilus edulis and M. californianus). This results shows another example of how the ecological extinction of a keystone predator can reduce species diversity in an ecosystem. The threshold of ecological extinction has passed due to over fishing so that local extinctions of the California spiny lobster are common.

Commercial oyster fishing had not affected the Chesapeake Bay ecosystem until mechanical dredges were utilized in the 1870s, resulting in overfishing of the oysters. The bay today is plagued by eutrophication due to algal blooms, and the resulting water is highly hypoxic. These algal blooms have competitively excluded any other species from surviving, including the rich diversity in faunal life that once flourished such as dolphins, manatees, river otters, sea turtles, alligators, sharks, and rays. This highlights the top-down loss of diversity commercial fishing has on marine ecosystems by removing the keystone species of the environment.